This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. MODELLER is a package for comparative modeling of proteins and complexes, developed and maintained in the Sali lab. It is additionally used as the base for a large number of lab projects, such as MODBASE and MODPIPE, and is made freely available for academic use. Web interfaces to several important modules of MODELLER, such as the comparative modeling itself, alignment tools, or ab initio loop refinement, are also in development. It is our desire to make MODELLER easy to use, fast, and flexible enough to be applied to new problems, such as docking of comparative models. We wish to make MODELLER available on the platforms used by our users, such as Alpha;socrates would thus be used on an occasional basis to compile, benchmark, and test Alpha builds of MODELLER. Additionally, in the interests of ease of use and improved interoperability, work is ongoing in converting MODELLER from a monolithic FORTRAN application into a set of Python and C modules for comparative modeling, using standard file formats and representations. The integration between MODELLER and other Python-based packages, such as CGL's own Chimera software, would be tested on these systems.